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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: May 29, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

PDBToSDF: Create ligand structure files from PDB file.

Naresh Babu Muppalaneni, Allam Appa Rao

    Bioinformation
    |September 10, 2011
    PubMed
    Summary

    PDBToSDF is a new tool that easily separates ligand data from Protein Data Bank (PDB) files. This enables straightforward calculation of essential ligand properties for drug discovery.

    Area of Science:

    • Biochemistry
    • Structural Biology
    • Cheminformatics

    Background:

    • Protein Data Bank (PDB) files store atomic data for protein-ligand complexes.
    • Structure Data File (SDF) formats contain molecular data for ligands, including atoms, bonds, and coordinates.
    • Analyzing ligand properties is crucial in understanding molecular interactions.

    Purpose of the Study:

    • To introduce PDBToSDF, a novel computational tool.
    • To facilitate the extraction of ligand information from PDB files.
    • To simplify the calculation of key ligand properties.

    Main Methods:

    • Development of the PDBToSDF tool.
    • Utilizing PDB files as input.
    • Separating ligand atomic data from protein data.
    Keywords:
    Molecular weightProtein Data Bank fileStructure Data file

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    Related Experiment Videos

    Last Updated: May 29, 2026

    Modeling Ligands into Maps Derived from Electron Cryomicroscopy
    09:30

    Modeling Ligands into Maps Derived from Electron Cryomicroscopy

    Published on: July 19, 2024

    Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
    08:49

    Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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  • Generating SDF files containing ligand-specific information.

    • Main Results:

    • PDBToSDF successfully isolates ligand data from PDB files.
    • The tool enables easy calculation of molecular weight.
    • Facilitates determination of hydrogen bond acceptors and donors for ligands.

    Conclusions:

    • PDBToSDF streamlines the process of ligand property calculation.
    • This tool aids researchers in drug discovery and molecular modeling.
    • Efficient ligand analysis is critical for advancing biochemical research.